Christoph,
I think I figured why there is no log msg for critical csg_stat in
calc_rdfgeneric.sh.
The fact is I override the inverse.sh script with the one having this (to
avoid all the frame numbers when reading trajectory files):
log="${PWD}/${log##*/}"
export CSGLOG="$log"
if [[ -f $CSGLOG ]]; then
exec 3>&1 4>&2 >> "$CSGLOG" 2>&1
echo -e "\n\n##################################"
# echo "# Appending to existing logfile #"
echo "# Appending to logfile (+errors) #"
echo -e "##################################\n\n"
msg --color blue "Appending to existing logfile (+errors)
${CSGLOG##*/}"
else
exec 3>&1 4>&2 >> "$CSGLOG" 2>/dev/null
echo -e "\n\n##################################"
echo "# Creating new logfile (-errors) #"
echo -e "##################################\n\n"
msg "For a more verbose log see: ${CSGLOG##*/} (or csg_inverse.log)"
fi
This worked before and did not affect the workflow.
Andrey
On Mon, Jul 23, 2018 at 1:50 PM, Christoph Junghans <[email protected]>
wrote:
> On Mon, Jul 23, 2018 at 6:46 AM, 'Andrey Brukhno' via votca
> <[email protected]> wrote:
> > Sorry, I forgot - below is the output of `grep critical inverse.log' for
> one
> > iteration:
> >
> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p
> topol.top
> > -o topol.tpr -c conf.gro'
> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p
> topol.top
> > -o topol.tpr -c conf.gro'
> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p
> topol.top
> > -o topol.tpr -c conf.gro'
> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p
> topol.top
> > -o topol.tpr -c conf.gro'
> > Running critical command 'mpirun -n 4 mdrun_mpi -s topol.tpr -c
> confout.gro
> > -o traj.trr -x traj.xtc -cpi state.cpt -maxh 47.8289 -multidir sim_0
> sim_1
> > sim_2 sim_3 -tablep table.xvg -tableb table_b1.xvg table_b2.xvg
> table_b3.xvg
> > table_b4.xvg table_b5.xvg table_a1.xvg table_a2.xvg table_a3.xvg
> > table_a4.xvg table_a5.xvg table_d1.xvg table_d2.xvg table_d3.xvg
> > table_d4.xvg table_d5.xvg table_d6.xvg'
> > Doing: critical csg_stat --nt 4 --options
> > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-
> freeN-dihs_CG-fits1-151cNT/dopc_cg-int-map11.xml
> > --top topol-rdf.tpr --trj traj.xtc --begin 0 --first-frame 0
> --block-length
> > 1000000 --ext dist.block --cg
> > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-
> freeN-dihs_CG-fits1-151cNT/dopc_cg-map11.xml;
> >
> > As you can see, the only mention of `critical csg_stat' is due to my
> > addition of echo.
> Well, the other lines with "Running critical command" show that the
> logging actually works.
> Did you overload calc_rdf_generic.sh with your own version?
> Otherwise, I would say your installation is bourked up.
>
> Christoph
> >
> > Andrey
> >
> > On Monday, July 23, 2018 at 1:17:32 PM UTC+1, Christoph Junghans wrote:
> >>
> >> On Mon, Jul 23, 2018 at 2:39 AM, 'Andrey Brukhno' via votca
> >> <[email protected]> wrote:
> >> >
> >> > On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans <
> [email protected]>
> >> > wrote:
> >> >>
> >> >> On Sun, Jul 22, 2018 at 1:27 PM, 'Andrey Brukhno' via votca
> >> >> <[email protected]> wrote:
> >> >> > Thanks for your reply Christoph.
> >> >> >
> >> >> > I did check it, but inverse.log does not contain sufficient info,
> see
> >> >> > the
> >> >> > extract below.
> >> >> > I will be investigating it further to make sure I did not do
> anything
> >> >> > stupid
> >> >> > myself, although I haven't changed much for the test iteration
> except
> >> >> > recompiling the tpr files for the newer version of Gromacs).
> >> >> The " rdf calculation is already done" tells me that this is not a
> run
> >> >> from scratch.
> >> >> Try a fresh run, because some chance in the xml don't get populated
> >> >> until the next iteration step.
> >> >> And grep for "csg_stat" (not rdf), you should see actually command,
> >> >> which got run, e.g.:
> >> >> "Running critical command 'csg_stat --nt 4 --options settings.xml
> >> >> --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0' "
> >> >> From that you can see if all the options are read as excepted.
> >> >>
> >> >
> >> > I knew you were going to say this...
> >> > As a matter of fact, there is no such message from
> calc_rdf_generic.sh,
> >> > but
> >> > instead:
> >> >
> >> > msg "Calculating rdfs with csg_stat using $tasks tasks"
> >> > critical csg_stat --nt $tasks --options "$CSGXMLFILE" --top "$topol"
> >> > --trj
> >> > "$traj" --begin $equi_time --first-frame $first_frame ${error_opts}
> >> > ${maps:+--cg ${maps}}
> >> > mark_done "rdf_calculation${suffix}"
> >> Well the "critical" function includes the print statement:
> >> critical() {
> >> [[ $quiet = "no" ]] && echo "Running critical command '$*'" >&2
> >> "$@" || die "${FUNCNAME[0]}: '$*' failed"
> >> }
> >> So I am not sure when that got lost in your case.
> >> >
> >> > so I had to add this after the msg and before the csg_stat call:
> >> > echo "Doing: critical csg_stat --nt $tasks --options "$CSGXMLFILE"
> >> > --top
> >> > "$topol" --trj "$traj" --begin $equi_time --first-frame $first_frame
> >> > ${error_opts} ${maps:+--cg ${maps}}"
> >> >
> >> > This shows me that topol-rdf.tpr is actually used (extract from
> >> > inverse.log):
> >> >
> >> > Make update for ibi
> >> > Calculating rdfs with csg_stat using 4 tasks
> >> > Doing: critical csg_stat --nt 4 --options
> >> >
> >> > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-
> freeN-dihs_CG-fits1-151cT/dopc_cg-int-map11.xml
> >> > --top topol-rdf.tpr --trj traj.xtc --begin 0 --first-frame 0
> >> > --block-length
> >> > 1000000 --ext dist.block --cg
> >> >
> >> > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-
> freeN-dihs_CG-fits1-151cT/dopc_cg-map11.xml;
> >> > begin to calculate distribution functions
> >> >
> >> > However, the distributions are still wrong, and I am lost now as to
> >> > which
> >> > program to blame (again all the initial files are the same as in my
> >> > previous
> >> > iteration).
> >> > I compared the outputs of `gmx dump topol-rdf.tpr' and `gmx dump
> >> > topol.tpr'
> >> > generated with the new Gromacs and everything seems alright, the
> >> > relevant
> >> > differences in exclusion lists are there.
> >> > The problem is also that the original calculation was done on a
> cluster
> >> > more
> >> > than a year ago, so I cannot reproduce exactly all the installation
> >> > setup,
> >> > not on my desktop anyway. But I know that those calculations were
> >> > correct
> >> > and well converged.
> >> >
> >> > So something should have changed somewhere within the newly installed
> >> > Gromacs/VOTCA combination.
> >> You can see what VOTCA has with:
> >> csg_dump --top topol-rdf.tpr --cg dopc_cg-map11.xml
> >>
> >> Remember, if you are using a mapping file ("--cg" option) exclusions
> >> from the topology file are ignored and the ones from the mapping file
> >> are used instead.
> >>
> >> Christoph
> >> >
> >> > Andrey
> >> >
> >> >> Christoph
> >> >> >
> >> >> > Andrey
> >> >> > -----
> >> >> > $ grep rdf inverse.log
> >> >> > ...
> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr
> table_??.xvg
> >> >> > index.ndx* conf.gro*'
> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr
> table_??.xvg
> >> >> > index.ndx* conf.gro*'
> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr
> table_??.xvg
> >> >> > index.ndx* conf.gro*'
> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr
> table_??.xvg
> >> >> > index.ndx* conf.gro*'
> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr
> table_??.xvg
> >> >> > index.ndx* conf.gro*'
> >> >> > ‘sim_0/topol-rdf.tpr’ -> ‘./topol-rdf.tpr’
> >> >> > Calculating rdfs with csg_stat using 4 tasks
> >> >> > Calculating average rdfs and its errors for interaction TCH-TCH
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCH-TCO
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCO-TCO
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCH-PO
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCH-NH
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCO-PO
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction TCO-NH
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction PO-PO
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction PO-NH
> >> >> > rdf calculation is already done
> >> >> > Calculating average rdfs and its errors for interaction NH-NH
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Sun, Jul 22, 2018 at 1:26 PM, Christoph Junghans
> >> >> > <[email protected]>
> >> >> > wrote:
> >> >> >>
> >> >> >> On Sat, Jul 21, 2018 at 9:01 PM, 'Andrey Brukhno' via votca
> >> >> >> <[email protected]> wrote:
> >> >> >> > Hello,
> >> >> >> >
> >> >> >> > I encountered a very strange (looks like legacy) issue with
> >> >> >> > v1.4.1.
> >> >> >> > In my earlier IBI iterations (with v1.3) I normally used special
> >> >> >> > topol-rdf.tpr which was different from normal CG simulation
> >> >> >> > topol.tpr
> >> >> >> > by
> >> >> >> > not
> >> >> >> > including the intra-molecular pairs in the RDF stats (done by
> >> >> >> > csg_stat).
> >> >> >> > I
> >> >> >> > wanted to make sure my previous results are reproduced by
> v1.4.1,
> >> >> >> > so
> >> >> >> > copied
> >> >> >> > all the initialisation files into a new directory and tried to
> run
> >> >> >> > once
> >> >> >> > again. After the very first iteration I checked the obtained
> RDFs
> >> >> >> > and
> >> >> >> > they
> >> >> >> > were all wrong - corresponding to normal topol.tpr (including
> >> >> >> > intra-pairs)
> >> >> >> > and not topol-rdf.tpr (excluding intra-pairs)!
> >> >> >> >
> >> >> >> > I guess there might have been changes made to locations or names
> >> >> >> > of
> >> >> >> > tags
> >> >> >> > in
> >> >> >> > settings.xml between the VOTCA versions, but I could not
> identify
> >> >> >> > those
> >> >> >> > changes by referring to the most recent manual (both v1.4.1 and
> >> >> >> > development
> >> >> >> > versions).
> >> >> >> >
> >> >> >> > Below is the relevant extract from my settings.xml file.
> >> >> >> >
> >> >> >> > Any clue, hint, advice are most welcome!
> >> >> >> We haven't changes any tags in IBI since v1.4.1 and the special
> >> >> >> topology for IBI can be set by cg.inverse.<sim_prog>.rdf.topol,
> >> >> >> which
> >> >> >> you did below.
> >> >> >> You could try "grep csg_stat inverse.log" to figure out if the
> right
> >> >> >> topology got appended to the command line of csg_stat.
> >> >> >>
> >> >> >> Christoph
> >> >> >> >
> >> >> >> > Thanks in advance.
> >> >> >> > Andrey
> >> >> >> >
> >> >> >> > -----------
> >> >> >> > <gromacs>
> >> >> >> > <grompp>
> >> >> >> > <bin>gmx grompp</bin>
> >> >> >> > <!--opts></opts-->
> >> >> >> > </grompp>
> >> >> >> > <mdrun>
> >> >> >> > <!--command>grmx-vtc-rerun.sh</command-->
> >> >> >> > <!--command>mpirun -lsf mdrun_mpi</command-->
> >> >> >> > <!--opts>-multidir sim_0 sim_1 sim_2 sim_3</opts-->
> >> >> >> > <command>mpirun -n 4 mdrun_mpi</command>
> >> >> >> > <opts>-multidir sim_0 sim_1 sim_2 sim_3 -tablep
> table.xvg
> >> >> >> > -tableb
> >> >> >> > table_b?.xvg table_a?.xvg table_d?.xvg</opts>
> >> >> >> > </mdrun>
> >> >> >> > <!--mdrun><opts>-nt 2</opts></mdrun-->
> >> >> >> > <!-- trash so many frames at the beginning -->
> >> >> >> > <equi_time>0</equi_time>
> >> >> >> > <!-- grid for table*.xvg !-->
> >> >> >> > <table_bins>0.001</table_bins>
> >> >> >> > <!-- cut the potential at this value (gromacs bug) -->
> >> >> >> > <pot_max>10000</pot_max>
> >> >> >> > <!-- extend the tables to this value -->
> >> >> >> > <table_end>2.5</table_end>
> >> >> >> > <initial_configuration>maindir</initial_configuration>
> >> >> >> > <rdf>
> >> >> >> > <block_length><DESC>Length of the block for the error
> >> >> >> > analysis</DESC>
> >> >> >> > 1000000
> >> >> >> > </block_length>
> >> >> >> > <map><DESC>Special mapping file for rdf calculations
> >> >> >> > needed
> >> >> >> > for
> >> >> >> > bonded interactions</DESC>
> >> >> >> > dopc_cg-map11.xml
> >> >> >> > </map>
> >> >> >> > <topol><DESC> Gromacs binary topol (tpr) file to be used
> >> >> >> > for
> >> >> >> > csg_stat</DESC>
> >> >> >> > topol-rdf.tpr
> >> >> >> > </topol>
> >> >> >> > <with_errors>yes<DESC>calculate error on the rdf:
> >> >> >> > yes/no</DESC>
> >> >> >> > </with_errors>
> >> >> >> > </rdf>
> >> >> >> > </gromacs>
> >> >> >> > -----------
> >> >> >> >
> >> >> >> > --
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> >> >> >> > Groups
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> it,
> >> >> >> > send
> >> >> >> > an
> >> >> >> > email to [email protected].
> >> >> >> > To post to this group, send email to [email protected].
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> >> >> >> > For more options, visit https://groups.google.com/d/optout.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Christoph Junghans
> >> >> >> Web: http://www.compphys.de
> >> >> >>
> >> >> >> --
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> >> >> >
> >> >> > --
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> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
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> >> >
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> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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